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Q9LTX3

- PPOX1_ARATH

UniProt

Q9LTX3 - PPOX1_ARATH

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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase 1, chloroplastic

Gene

PPOX1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP). Involved in the PLP salvage pathway. Has a higher preference for PNP over PMP. May also catalyze the epimerization of the S- and R-forms of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration. This is a prerequisite for the S-specific NAD(P)H-hydrate dehydratase to allow the repair of both epimers of NAD(P)HX.2 Publications

Catalytic activityi

Pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + H2O2.
Pyridoxine 5'-phosphate + O2 = pyridoxal 5'-phosphate + H2O2.
(R)-NADHX = (S)-NADHX.

Cofactori

Protein has several cofactor binding sites:
  • FMNBy similarityNote: Binds 1 FMN per subunit.By similarity
  • K(+)By similarityNote: Binds 1 potassium ion per subunit.By similarity

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi132 – 1321PotassiumBy similarity
Metal bindingi196 – 1961PotassiumBy similarity
Binding sitei238 – 2381NAD(P)HXBy similarity
Metal bindingi241 – 2411PotassiumBy similarity
Binding sitei374 – 3741FMNBy similarity
Binding sitei377 – 3771FMN; via amide nitrogenBy similarity
Binding sitei379 – 3791SubstrateBy similarity
Binding sitei396 – 3961FMNBy similarity
Binding sitei436 – 4361SubstrateBy similarity
Binding sitei440 – 4401SubstrateBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi389 – 3902FMNBy similarity
Nucleotide bindingi453 – 4542FMNBy similarity

GO - Molecular functioni

  1. FMN binding Source: InterPro
  2. metal ion binding Source: UniProtKB-KW
  3. NADHX epimerase activity Source: TAIR
  4. NADPHX epimerase activity Source: TAIR
  5. pyridoxamine-phosphate oxidase activity Source: TAIR

GO - Biological processi

  1. NADH metabolic process Source: TAIR
  2. NADP metabolic process Source: TAIR
  3. pyridoxal metabolic process Source: TAIR
  4. pyridoxal phosphate biosynthetic process Source: GOC
  5. pyridoxine biosynthetic process Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Oxidoreductase

Keywords - Biological processi

Pyridoxine biosynthesis

Keywords - Ligandi

Flavoprotein, FMN, Metal-binding, NAD, Nucleotide-binding, Potassium

Enzyme and pathway databases

BioCyciARA:AT5G49970-MONOMER.
MetaCyc:MONOMER-17901.
UniPathwayiUPA00190; UER00304.
UPA00190; UER00305.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxine/pyridoxamine 5'-phosphate oxidase 1, chloroplastic
Short name:
AtPPOX1
Including the following 2 domains:
Alternative name(s):
PNP/PMP oxidase
Short name:
PNPOx
Pyridoxal 5'-phosphate synthase
Probable NAD(P)HX epimerase (EC:5.1.99.-)
Gene namesi
Name:PPOX1
Synonyms:PDX3, PDXH
Ordered Locus Names:At5g49970
ORF Names:K9P8.11
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548: Chromosome 5

Organism-specific databases

TAIRiAT5G49970.

Subcellular locationi

Plastidchloroplast 1 Publication

GO - Cellular componenti

  1. chloroplast Source: TAIR
  2. cytosol Source: TAIR
  3. mitochondrion Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 6363ChloroplastSequence AnalysisAdd
BLAST
Chaini64 – 530467Pyridoxine/pyridoxamine 5'-phosphate oxidase 1, chloroplasticPRO_0000420549Add
BLAST

Proteomic databases

PRIDEiQ9LTX3.

Expressioni

Tissue specificityi

Expressed in leaves, stems, flowers and roots.1 Publication

Inductioni

Circadian regulation. Up-regulated by light, heat, jasmonic acid, ethylene and abscisic acid treatments. Down-regulated by drought and salt treatment. Not induced by UV irradiation.1 Publication

Gene expression databases

GenevestigatoriQ9LTX3.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi3702.AT5G49970.1-P.

Structurei

3D structure databases

ProteinModelPortaliQ9LTX3.
SMRiQ9LTX3. Positions 73-309, 337-530.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini81 – 297217YjeF N-terminalAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni131 – 1355NAD(P)HXBy similarity
Regioni200 – 2067NAD(P)HXBy similarity
Regioni321 – 3244Substrate bindingBy similarity
Regioni505 – 5073Substrate bindingBy similarity

Domaini

Most plant PPOX proteins have both a pyridoxamine 5'-phosphate oxidase domain and an extra YjeF N-terminal domain.

Sequence similaritiesi

In the N-terminal section; belongs to the NnrE/AIBP family.Curated
In the C-terminal section; belongs to the pyridoxamine 5'-phosphate oxidase family.Curated
Contains 1 YjeF N-terminal domain.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000243404.
KOiK00275.
K17759.
OMAiCVRIGKP.
PhylomeDBiQ9LTX3.

Family and domain databases

Gene3Di2.30.110.10. 1 hit.
3.40.50.10260. 1 hit.
HAMAPiMF_01629. PdxH.
MF_01966. NADHX_epimerase.
InterProiIPR000659. Pyridox_Oxase.
IPR019740. Pyridox_Oxase_CS.
IPR011576. Pyridox_Oxase_FMN-bd.
IPR021198. Pyridox_Oxase_pln.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN-bd.
IPR004443. YjeF_N_dom.
[Graphical view]
PfamiPF10590. PNPOx_C. 1 hit.
PF01243. Pyridox_oxidase. 1 hit.
PF03853. YjeF_N. 1 hit.
[Graphical view]
PIRSFiPIRSF037048. PyrdxN_5-P_Oxase_ross-cont_pln. 1 hit.
SUPFAMiSSF50475. SSF50475. 1 hit.
SSF64153. SSF64153. 1 hit.
TIGRFAMsiTIGR00558. pdxH. 1 hit.
TIGR00197. yjeF_nterm. 1 hit.
PROSITEiPS01064. PYRIDOX_OXIDASE. 1 hit.
PS51385. YJEF_N. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q9LTX3-1) [UniParc]FASTAAdd to Basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MRNVIRRVTT MTFTFLLQSP PLPISPSPPQ FSLSSSPLSK TQRFITPSQG
60 70 80 90 100
SRLRTLCTKV IIPNMQDSGS PPLSYLTQRE AAEIDETLMG PLGFSIDQLM
110 120 130 140 150
ELAGLSVAAS IAEVYKPEEY SRVLAICGPG NNGGDGLVAA RHLHHFGYKP
160 170 180 190 200
FICYPKRTAK PLYTGLVTQL DSLSVPFVSV EDLPDDLSKD FDVIVDAMFG
210 220 230 240 250
FSFHGAPRPP FDDLIRRLVS LQNYEQTLQK HPVIVSVDIP SGWHVEEGDH
260 270 280 290 300
EDGGIKPDML VSLTAPKLCA KRFRGPHHFL GGRFVPPSVA EKYKLELPSY
310 320 330 340 350
PGTSMCVRIG KPPKVDISAM RVNYVSPELL EEQVETDPTV QFRKWFDEAV
360 370 380 390 400
AAGLRETNAM ALSTANKDKK PSSRMVLLKG FDENGFVWFT NYESKKGSDL
410 420 430 440 450
SENPSAALLF YWEILNRQVR IEGPVERIPE SESENYFHSR PRGSQIGAIV
460 470 480 490 500
SKQSSVVPGR HVLYDEYEEL TKQYSDGSVI PKPKNWGGFR LKPNLFEFWQ
510 520 530
GQPSRLHDRL QYSLQDVNGN PAWKIHRLAP
Length:530
Mass (Da):59,376
Last modified:October 1, 2000 - v1
Checksum:i22E8DFEC1A2167EE
GO
Isoform 2 (identifier: Q9LTX3-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     261-271: Missing.
     478-530: Missing.

Note: Not detected in roots.

Show »
Length:466
Mass (Da):52,042
Checksum:i3E2B851F982461E5
GO

Sequence cautioni

The sequence AAM65907.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAM83249.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti241 – 2411S → Y in AAM65907. 1 PublicationCurated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei261 – 27111Missing in isoform 2. CuratedVSP_044534Add
BLAST
Alternative sequencei478 – 53053Missing in isoform 2. CuratedVSP_044535Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB024032 Genomic DNA. Translation: BAA97018.1.
CP002688 Genomic DNA. Translation: AED95879.1.
CP002688 Genomic DNA. Translation: AED95878.1.
AY127025 mRNA. Translation: AAM83249.1. Different initiation.
BT000605 mRNA. Translation: AAN18174.1.
AY088368 mRNA. Translation: AAM65907.1. Different initiation.
RefSeqiNP_568717.2. NM_124376.3. [Q9LTX3-1]
NP_974918.1. NM_203189.1. [Q9LTX3-2]
UniGeneiAt.28155.

Genome annotation databases

EnsemblPlantsiAT5G49970.1; AT5G49970.1; AT5G49970. [Q9LTX3-1]
GeneIDi835061.
KEGGiath:AT5G49970.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB024032 Genomic DNA. Translation: BAA97018.1 .
CP002688 Genomic DNA. Translation: AED95879.1 .
CP002688 Genomic DNA. Translation: AED95878.1 .
AY127025 mRNA. Translation: AAM83249.1 . Different initiation.
BT000605 mRNA. Translation: AAN18174.1 .
AY088368 mRNA. Translation: AAM65907.1 . Different initiation.
RefSeqi NP_568717.2. NM_124376.3. [Q9LTX3-1 ]
NP_974918.1. NM_203189.1. [Q9LTX3-2 ]
UniGenei At.28155.

3D structure databases

ProteinModelPortali Q9LTX3.
SMRi Q9LTX3. Positions 73-309, 337-530.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 3702.AT5G49970.1-P.

Proteomic databases

PRIDEi Q9LTX3.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi AT5G49970.1 ; AT5G49970.1 ; AT5G49970 . [Q9LTX3-1 ]
GeneIDi 835061.
KEGGi ath:AT5G49970.

Organism-specific databases

TAIRi AT5G49970.

Phylogenomic databases

eggNOGi COG0259.
HOGENOMi HOG000243404.
KOi K00275.
K17759.
OMAi CVRIGKP.
PhylomeDBi Q9LTX3.

Enzyme and pathway databases

UniPathwayi UPA00190 ; UER00304 .
UPA00190 ; UER00305 .
BioCyci ARA:AT5G49970-MONOMER.
MetaCyc:MONOMER-17901.

Gene expression databases

Genevestigatori Q9LTX3.

Family and domain databases

Gene3Di 2.30.110.10. 1 hit.
3.40.50.10260. 1 hit.
HAMAPi MF_01629. PdxH.
MF_01966. NADHX_epimerase.
InterProi IPR000659. Pyridox_Oxase.
IPR019740. Pyridox_Oxase_CS.
IPR011576. Pyridox_Oxase_FMN-bd.
IPR021198. Pyridox_Oxase_pln.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN-bd.
IPR004443. YjeF_N_dom.
[Graphical view ]
Pfami PF10590. PNPOx_C. 1 hit.
PF01243. Pyridox_oxidase. 1 hit.
PF03853. YjeF_N. 1 hit.
[Graphical view ]
PIRSFi PIRSF037048. PyrdxN_5-P_Oxase_ross-cont_pln. 1 hit.
SUPFAMi SSF50475. SSF50475. 1 hit.
SSF64153. SSF64153. 1 hit.
TIGRFAMsi TIGR00558. pdxH. 1 hit.
TIGR00197. yjeF_nterm. 1 hit.
PROSITEi PS01064. PYRIDOX_OXIDASE. 1 hit.
PS51385. YJEF_N. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence features of the regions of 3,076,755 bp covered by sixty P1 and TAC clones."
    Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H., Tabata S.
    DNA Res. 7:31-63(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  2. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  3. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 12-530 (ISOFORM 1).
    Strain: cv. Columbia.
  4. "Full-length cDNA from Arabidopsis thaliana."
    Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
    Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 34-530 (ISOFORM 1).
  5. "Identification of a pyridoxine (pyridoxamine) 5'-phosphate oxidase from Arabidopsis thaliana."
    Sang Y., Barbosa J.M., Wu H., Locy R.D., Singh N.K.
    FEBS Lett. 581:344-348(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS PYRIDOXINE/PYRIDOXAMINE 5'-PHOSPHATE OXIDASE, CATALYTIC ACTIVITY.
  6. "Vitamer levels, stress response, enzyme activity, and gene regulation of Arabidopsis lines mutant in the pyridoxine/pyridoxamine 5'-phosphate oxidase (PDX3) and the pyridoxal kinase (SOS4) genes involved in the vitamin B6 salvage pathway."
    Gonzalez E., Danehower D., Daub M.E.
    Plant Physiol. 145:985-996(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS PYRIDOXINE/PYRIDOXAMINE 5'-PHOSPHATE OXIDASE, CATALYTIC ACTIVITY.
  7. "Expression, in vivo localization and phylogenetic analysis of a pyridoxine 5'-phosphate oxidase in Arabidopsis thaliana."
    Sang Y., Locy R.D., Goertzen L.R., Rashotte A.M., Si Y., Kang K., Singh N.K.
    Plant Physiol. Biochem. 49:88-95(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, INDUCTION, ALTERNATIVE SPLICING, SUBCELLULAR LOCATION.

Entry informationi

Entry nameiPPOX1_ARATH
AccessioniPrimary (citable) accession number: Q9LTX3
Secondary accession number(s): F4K7H2, Q8L7T7, Q8L9L3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 9, 2013
Last sequence update: October 1, 2000
Last modified: November 26, 2014
This is version 104 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

Mutants with reduced expression of PPOX1 (RNAi) have lower levels of total B6 vitamers, a reduced growth and are sensitive to high light.1 Publication

Keywords - Technical termi

Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3